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1 Supporting information 2 PCR amplification and DGGE analysis 3 The samples were initially subjected to DGGE analysis. 16S rRNA genes from different 4 samples were amplified through nested PCR using the following general bacterial primer 5 combinations: 6 (5′-GGTTACCTTGTTACGACTT-3′) 7 PCR-DGGE, a GC clamp was attached to the 5′-end of the 968F primer. The 8 primary/secondary PCR reactions were performed on a TC-512 automated thermal cycler 9 (Techne, UK) under the following cycling conditions: initial denaturation at 94 °C for 4 min, 10 followed by 30 cycles of 30 s denaturation at 94 °C, 30 s annealing at 53 °C for primary and 11 57 °C for secondary PCR, and 90 s for primary and 40 s for secondary PCR elongation at 12 72 °C, and a final 6 min extension at 72 °C. These PCR amplifications were carried out in 13 quadruplicate 25 mL reactions using the following reagents: ~5 ng bacterial genomic DNA or 14 PCR products, 0.4 μM of each primer, 0.2 mM of each dNTP solution, 1 × PCR reaction 15 buffer, 0.6 U of TaKaRa Ex Taq DNA polymerase (TaKaRa Corporation Ltd., Dalian, China), 16 and double-distilled water to a final volume of 25 μL. 27F (5′-AGAGTTTGATCCTGGCTCAG-3′)-1492R (primary) and 968F-1401R (secondary). For 17 DGGE profiling was performed on a Dcode universal mutation detection system 18 (Bio-Rad laboratories Inc., USA) according to the manufacturer's instructions. The PCR 19 products were loaded onto 8% (w/v) polyacrylamide gels in 1× TAE buffer (40 mM Tris-HCl, 20 40 mM acetic acid, and 1 mM EDTA; pH 8.4). The polyacrylamide gels were prepared with a 21 denaturing gradient ranging from 42% to 60% (100% denaturant contains 7 M urea and 40% 22 formamide) to obtain the best discrimination between bacterial species. After electrophoresis, 23 the gels were stained for 30 min with silver nitrate in TAE buffer, rinsed, and then 24 photographed. 25 PCR amplification and T-RFLP analysis 26 For T-RFLP analysis, the PCR primers (27F and 1492R) were used; the amplification 27 conditions are as described above. The primer 27F was fluorescently labeled on its 5′-end 28 with carboxifluorescein (5′-/6-FAM), and Blend Taq-plus polymerase (Toyobo, Japan) was 29 used instead of Ex Taq polymerase. The products from three independent amplifications were 30 pooled for each sample. The pooled PCR products were digested with Mung bean nuclease 31 (TaKaRa Corporation Ltd., China) to remove the single-stranded extensions. The digestion 32 products were then purified using a DNA purification Kit (Axygen, China) according to 33 manufacturer's recommendations. 34 Approximately 200 ng of the 16S rRNA gene amplification product from each sample 35 was digested with restriction endonucleases HaeIII (15 U), MspI (10 U), or HhaI (10 U) 36 (Fermentas, China) for 15 min at 37 °C. The digested fragments were purified using a DNA 37 purification Kit (Axygen, China). The efficiency of restriction digestion was evaluated by 38 agarose gel electrophoresis. Afterwards, the fluorescently labeled fragments were separated 39 on a 3730 DNA Analyzer (Applied Biosystems, USA). The sizes of the fragments were 40 determined by comparison with the internal GeneScan™ 500 LIZ® Size Standard. Three 41 independent replicate T-RFLPs were done for each 16S rRNA gene amplification. 42 The length of each terminal restriction fragment (TRF) sequence was visualized using 43 GeneMapper® Software v4.1 (Applied Biosystems, USA). The following procedures were 44 followed to obtain TRFs: the TRF sizes should lie in 50 bp and 500 bp, TRFs with fluorescent 45 units (FU) not exceeding 200 were excluded, and two peaks were regarded as the same if the 46 difference in the peak size was less than 1 nt. In addition, a 0.5% relative abundance threshold 47 was applied, and the TRFs with areas less than the threshold were removed from the 48 remaining analyses. Each unique TRF was considered an OTU. Only those TRFs presented 49 twice in three independent replicate of each 16S rRNA gene amplification were considered 50 valid TRFs. 51